Dark Destiny
by XxdangerousfangirlxX
Summary: Sebastian comes back for Clary. He threatens her to either run away with him and burn down the world or she will watch the love of her life die. What will she choose? War is declared. It will be a dramatic turn of events in The Mortal Instruments series. Will Sebastian finally be taken down? Will Clace survive the chaos? Some must die, so others can live. Who will they be?
1. Prologue

#DarkDestinyFanfic

Prologue

Sebastian's POV: I have a plan. A plan of revenge. Surely, I was deeply upset with Clary's friends for ruining everything. I was one second away from creating my own evil army. Clary and her friends ruined it. They are going to have to pay. I forgive Clary, clearly, because she is my sister. We are the last of the Morgenstern's. She will stand by my side whether she likes it or not. I was now walking down a dark alley near an abandoned hotel, Hotel Dumort. U was also now changed into gear. Don't ask where I got it from. I kept walking until a shadow appeared a few feet away from me. It was a person. "What are you doing here at night? Here, precisely?" It asked. Spanish accent, clearly. "That's none of your concern. I am just simply walking down here to say hi to a rat or two." I snapped sarcastically. "Uye, you're a feisty one. I am Raphael, head of the New York vampire clan." He said and took a few steps towards me. I was finally able to see his face. "Not bad. I am Jonathan, but everyone calls me Sebastian. If you want to, call me a Shadowhunter. I don't see myself as one. I have more demons inside me that the ones I want by my side. I am different from Nephilim." I explained. "Bueno, Sebastian or Jonathan, whatever, you could be useful to me." He said. "What is it you need me for? To run a lemonade stand? Whiten your teeth after a bloody dinner? I am not interested it any of your deals." I snapped. "Oh porfavor, you will be by my side after I tell you this. I know what you might want to do. Kill those fellow shadowhunters from the New York institute. You want to burn down the world, will all humans in it. Trust me, I know how you feel. I can help you, if you let me." He said. I inhaled deeply. "You're smarter than I thought Raphael. Let's say we can make a deal? You and your vampire clan can help me attack the New York Institute tonight so I can run away with my sister. Then, I might help you as well. Will you do it?" I asked. "We cannot step into the institute. It's-" I cut him off and said "You can't possibly know what will happen if no one ever did it?" I asked. He thought about it for a moment and finally said "You have a point there Jonathan, let's do it." "By the way, don't blame me if you lose some of yours. Not my fault they're weak." I said. He snorted and said "Fine, so we have a deal?" He held out his pale hand. I looked at it and then back at him. "We have a deal." I said and shook his hand. He grinned and looked behind me. "Are you ready?" Tonight will get dirty." He said. I looked over my shoulder to see a lot of vampires ready to fight. I looked back at Raphael. "We have excellent hearing and they wouldn't want to disobey their master. They know what happens to them." He said. "Okay now let's go." I said as we started to walk down the alley. "I actually like you Jonathan, unlike others of your kind." Raphael said. I smirked and said "I am the only one of my kind."


	2. Chapter 1

**Hey guys, I am new at this so I am going to make a quick author's note. I will try and update every week OR every day. I do have school, so I have to study and do homework. I will try hard to make every chapter long and dramatic so you guys like it. I hope you liked the prologue! Okay, well, here goes nothing. Chapter one. **

Clary's POV

Everything had gone back to normal, not that I remember what exactly "normal" is anymore. Jace still has the heavenly fire in him. Isabelle had declared her feelings for Simon, so basically; they were now officially a couple. They were out on a date tonight, or somewhere else, who knows. Alec had moved back in the institute, due to the fact Magnus broke up with him. He hasn't taken it very well. He was at the moment, locked in his room, like always. I was in the institute library drawing in my sketchpad. Drawing runes, trying to come up with new ones, just in case we needed some help one of these months. I couldn't focus. I suddenly heard someone coming downstairs. It was probably Jace. I turned to doodling sketches again.

"Clary?" It was Alec.

I turned to look at him over my shoulder. He looked way different. Dark lines were noticeable under his eyes. His hair was messier than ever. His eyes were dark blue. He was wearing baggy clothes and looked tired than ever.

"Yeah? Alec are you okay?" I asked with concern.

"I don't know. I just need to focus my mind on something to forget about...A-about...-"His voice broke as he took a seat on the leather chair beside me.

"I am sorry this had to happen. I am sure he will come around at some point. It's not like he could live without you." I said and set down my notebook and pencil on the table.

"Yeah, right, is that what he said when he was with Will? I am sure I was just trivial for him. I don't know what to think at this point anymore Clary." He said as he stared into nothing in particular. I didn't say anything. I didn't know what to say.

"Maybe you just have to wait." I finally said. Alec's eyes slowly closed as a tear ran down his pale cheek.

"Wow, Alec and Clary are actually bonding? What did I miss out on the whole time I was gone?" Jace came in asking sarcastically. I rolled my eyes. Alec buried his face in his hands.

"Are you okay bro?" Jace asked as he was about to put his hand on his shoulder but snatched it back. _How long will Jace be able to live like this? _ I thought to myself. He smiled at me as I smiled back. We have slowly started to drift away these past couple of weeks.

"I am fine. While Magnus is off somewhere falling in love with another person, yeah, I am totally fine." He said.

"Don't say that okay? Don't do this to yourself." Jace said. Alec's face was still buried in his face.

"It could have been a lot worse, right?" I asked. Alec shrugged. "Let's forget about that for a while. Um, do you think we could go to Taki's?" Jace asked.

"I am not hungry." Alec and I said together at the same time. Jace rolled his eyes. We all stopped talking for a moment. Everything stood still. Until screaming was heard from the hall of the institute.

"GUYS! ALEC! CLARY! JACE!" It was Isabelle.

Isabelle came in running into the library, out of breath and in shock. Alec stood up to catch her as she collapsed on the ground. "I- I….s-saw-w…" She tried saying but failed, due to the fact she was trying to catch her breath. Jace and I stood there with wide eyes until Alec said "Who did you see? Izzy speak!"

"I saw Sebastian!" She yelled. Alec, Jace and I gasped. Horror filled my mind as I panicked. "I saw him near Hotel Dumort with an army of vampires. Simon and I saw them. They were heading somewhere. They are coming for us. Simon rushed to Luke's house. I ran here to tell you guys." She explained.

"No, this can't be happening." I said as I touched my forehead. I hadn't noticed I was sweating. Sebastian, my brother never meant to be, the one who was supposed to be dead, was alive and healthy out in Brooklyn, coming to get us. This was all happening too fast.

"They can't come in here, the vampires, it's-"Alec started but Jace cut him off.

"Well, do you plan on telling them that? They are coming here to get revenge. You know Sebastian…Jonathan I mean, he will never go down without a fight." Jace said.

Alec inhaled deeply.

"I'll go for weapons. Stay here okay? I'll be back." Jace said. Our eyes met for a second until he looked away and walked out of the library to the weapon's room. I looked back at Izzy and Alec. How I wish Sebastian and I could be like that. He is a monster, who will never be tamed. Izzy started to cry as Alec held her. I would start crying at any moment too, but a fight was about so start, no room left for my tears.

"Izzy-"I started but stopped as all the light of the institute shut down. Everything turned dark. Isabelle screamed.

"It's okay Iz, there must be something wrong with the electricity, it will be back on any second-"Alec said. The lights were turned back on a blink of an eye. We all sighed. We turned our heads to see a bunch of vampires, hungry and ready to attack. I gasped as Izzy screamed. A lot of them were showing their fangs. I took a few steps behind me as I stared at them wide eyed. Isabelle stood up and slowly took her whip out. Alec and I were left empty handed. They started to run to us until many of them were either slashed behind their backs or thrown to the ground or was either bitten. I recognized them from the moment I saw them, Luke and his pack. Izzy ran to them and slashed her whip on many of the vampire's heads and chests. "Guys go! Get weapons! I'll be safe!" Izzy yelled. Someone suddenly turned Alec and me around. I thought it was over until I saw that it was Jace. I sighed as Jace handed Alec his crossbow and a dagger. "Clary, run, get out of here, Sebastian will come for you any minute. Go, please." Jace pleaded as Alec ran towards the blood bath and fought as well.

"Jace no, I can't leave you, I won't leave you." I said as water started to fill my eyes.

He shook his head and pushed me towards the exit of the library. "I'll find you, I promise." He said. He took a step towards me and brushed my cheeks ever so softly with his fingers.

I didn't have time to say anything else before I caught myself running out of the library. I was now running down the hall of the institute. I ran towards the 2nd floor and into an empty room. I locked it shut with the lock. I looked around the room to notice I was in Jace's room. I shuffled through his drawers and finally found a stele. I walked over to the window seat. I pushed the window open. I peeked my head out of it and looked down. It didn't look that far down. The cold wind gave my skin Goosebumps. I pushed it all the way open as I seated myself on the edge. I took a deep breath and thought of what Jace had told me. _Go, get out of here. I will find you, I promise. _I gripped the edge of the window, stele in one hand and let myself fall as I closed my eyes. That was until somebody pulled me back by my arm. I looked over my shoulder to see him. Sebastian. "NO!" I yelled as I slipped off the edge and my body was hanging into the air. Sebastian gripped me hard on my wrists. I was breathing fast. I looked down and noticed it was actually far down. "No! Clary!" He yelled as my wrists were starting to slip off his grip. "No! Don't let me go!" I cried. What was I thinking of jumping off the 2nd floor of the institute? Sebastian finally pushed me up as I let myself back into the room. I ended up falling on top of Sebastian. He grinned as I looked at him closely. I pulled myself off from him quickly and stood back, away from him. He got up as well and said "Don't fear little sister, I won't kill you."

"And why should I trust you?" I said in a shaky voice.

"Because I am your brother." He said in a calmed voice.

I shook my head and said "You're dead to me."

He ignored my comment and said "I am here to tell you something. Something that will affect your life. I would have called you but as you see, I never got your phone number." He smirked.

"Ask and leave Sebastian. Harm my friends and you will be dead, I can promise you that." I said.

"Okay, then, I am here to tell you this, run away with me as we burn down the world together, or you can watch the love of your life die. I am not lying. I have the weapon, as always. Make the right choice dear sister." He said. All of those words ran through my head and found myself gasping for air.

**Tun tun tun! Dramatic huh? Anyways, I'll try to update soon! What do you think will happen? What do you think Clary's choice will be? Send in reviews! (:**


	3. Chapter 2

**Chapter 2 is here shadowhunters! I will really try to update as soon as I can. I love how many views my fan fiction is getting! I CAN'T EVEN! I love you guys! It makes me feel so happy (': Chapter 2…begins…now. **

Clary's POV

Was he seriously asking me this? This was happening all over again like it happened with Jace. Oh no.

"What?! Are you crazy? NO!" I yelled.

"shh, calm down little sister. Just make a choice." He said and stood still, waiting for me to answer.

I panted hard, due to the fact, I couldn't breathe. I felt lightheaded, like I was about to faint. I closed my eyes as I collapsed on the floor. I felt Sebastian catch me, he was indeed really fast.

"Clary? Are you okay?" He asked. I shook my head as I kept my eyes closed. I kept hoping this was all a dream. Unfortunately, it wasn't. I opened my eyes. My eyes met Sebastian's black eyes. I slowly sat up and buried my face in my hands. "You can't seriously be asking me this, _again._" I said.

"You know me very well little sister. You even know how my lips feel." He said and chuckled.

"Shut up and forget about that." I snapped.

"So what is it going to be little sister? Will you come with me and burn down the world, or do you want Jace to die? Your choice. But It will affect your life. Choose wisely little sister." He said.

I inhaled deeply and thought about it. _There will be a way out of this Clary. Do it, and save Jace._ I took a deep breath and said "Fine. I'll go with you."

He grinned and said "Good girl. Now let's go." He said as he walked towards the window.

"You can't be serious. Just after what happened? Do you expect me to believe you're a spider monkey now?" I asked.

"The things I can do my sister." He grinned. I scoffed as I walked to him.

"get on." He said. He was telling me to get on his back. I rolled my eyes and did it.I wrapped my arms around his chest. He held on to me from my ankles. He climbed to the edge of the window and asked "You ready?" I slowly nodded. "Okay, here we go." I closed my eyes as I we fell. I screamed but didn't open my eyes. The wind and pressure was too much for me. Heights were too much for me. Everything suddenly went black. I felt like I was drowning in darkness.

Jace's POV

I struck my dagger into a vampire's heart and kicked him onto the floor. Alec was beside me, fighting. Who knows where Isabelle went. A small group of vampires walked towards us. That's when I noticed him. Raphael. "Old _amigo_. So happy to see you again. May I ask, where is the short red headed girl?" he asked.

"She's gone!" I heard someone yell. Isabelle. She came down the stairs of the library as she panted. "She… she is gone. I am guessing Sebastian took her. What was left of her was a stele." She said.

"I can't believe this." I scoffed.

"Enough. Since Sebastian already left. We're not leaving here until we feed." He said. He took a vicious step towards me before Isabelle took out a gun and shot him right in the heart. He collapsed dead on the floor.

"NOW WHO IS NEXT!" She yelled to the group of vampires. They winced and ran out of the library. She looked at me and said "I am sorry but I was getting tired of all this."

"I would have done it too. So, Clary is gone?" I asked. She nodded sadly.

"I knew this was going to happen." I said as I sat down near the nearest chair with blood on it, I ignored it. "I promised I would find her, now that she is with Sebastian. I am not so sure that will be possible." I said.

"We can track him down with anything he left around here, a bit of hair, blood or-" Alec said but stopped talking as he passed me. He was looking at something near the library doors. I frowned and look at what he was looking at. I hadn't noticed who was walking down the library stairs. Magnus. I quickly stood up and rushed over to him. I threw him against the wall and said "What are you doing here downworlder?" He pushed me away, making me more furious. I was clearly furious that he broke my parabatai's heart, that's something I will never forgive.

"Calm down Blondie, okay? I heard that the vampires attacked you." He eyed something on the floor. He grinned and said "You killed Raphael huh?"

"I did actually, and if you don't leave, you're next." Izzy said and walked next to me. She folded her arms across her chest. She gave Magnus the glare that would send anyone jumping off a cliff. Like Alec, Isabelle has the same attitude like him.

"I am not afraid of you Nephilim. I suspected you needed my help. Why? Because Sebastian took Clary." He said.

"How do you know about that?" I asked.

"I saw them leaving here. He was carrying Clary unconscious. I couldn't chase them, they portaled somewhere. Both of them." Magnus said. I inhaled deeply at the words "_...- carrying Clary unconscious."_ I am guessing he knocked her out.

"We don't need your help Magnus." Alec finally said after all this time. He glared at Magnus as he walked next to Izzy and me. Magnus stood still. "You can leave, and never come back." He said.

Magnus looked at him with sad eyes and inhaled deeply. "Fine, but you'll be needing me I promise-"

"I promise you that you won't be welcome here again and you will not to be trusted ever again. Leave." Alec cut him off. Magnus took a deep breath and walked over back to the library doors. He took one last glance over his shoulder at Alec and walked out of the library. I looked at Alec to see him trying to fight back the tears.

"Alec-" Izzy started but Alec cut her off too.

"I am fine." He said as tears ran down his cheeks. "I need some time alone." He said and wiped his tears. He then walked out of the library, walking to his room, probably. I sighed and looked at Isabelle.

" I hate seeing him hurt." She said. "I swear on the angel I will _kill_ Magnus if anything ever happens to Magnus." She said as tears ran down her cheeks. She turned her hand into a fist and clenched her jaw. I pulled her to a hug to calm her down.

"Shh, calm down Izzy. Nothing will happen. Everything will be okay. For now we need to focus on finding that bastard of Sebastian. Then we'll get revenge on Magnus." I said. I closed my eyes as I rested my head on Izzy's head. _"I'll find you Clary. I don't care if I have to burn down the world myself. I will find you my love._"

**There you go! Chapter 2! How did you like it? What do you think will happen? I seriously got my feels killed as I wrote the tragic Malec scene D: I'll **_**try**_** and update soon! Don't get mad at me if I don't, I have school, homework, chores and stuff ._. Review? (:**


	4. Author's note!

**Sorry guys! This is a quick author's note. I am so sorry I haven't posted in a long time! I will try and update soon, I promise! The views on my fanfic are crazy! Thank you guys so much! It means a lot! I never thought this would happen! I will try and update tomorrow, hopefully! I have so much stuff to do! I am writing 3 fan fictions at a time, I have to post daily on my 3 instagram accounts and I have to study and do homework! Don't get mad if I don't update as soon as you guys want me to! Also, if any of you have questions for me, send me them! I am loving all of your reviews! It means a LOT to me that I am known for my amazing writing skills, so thank you! **

**I AM SO SORRY IF I DISSAPOINTED YOU BY MAKING YOU THINK THIS WAS THE NEXT CHAPTER! :/**


	5. Chapter 3

**Okay, now. I am sorry it took long to update this chapter but here it is now? Okay? Dum roll… and here is Chapter 3. **

THE NEXT DAY…

Clary's POV

I woke up from the darkness I was in. I was tangled in warm blankets. My head on a pillow. I was in a large bed in a bedroom. The room was quite large too. The walls were painted a faddish color of blue. The floor was wooden. The bed was in the middle of the room. There was a coffee table next to the bed and a closet in the corner of the room. There was a window on the other side of the bed. I slowly sat up, confused. Where was I? Why was I here? What had happened? That's when it hit me. I ran away with Sebastian. Him convincing me to run away with him. Both of us jumping out the room window. Me passing out. My head pounded hard. I moaned. I removed the blankets from my body. I slowly stood up. I was changed into different clothes. Blue shirt. Gray sweatpants. I frowned as I walked towards the door. I slowly turned the knob and walked into the hallway. The hallway was a dead end. It had more rooms. I silently made my way to the next room. I took a deep breath as I turned the knob and pushed the door open. The room was similar like the one I woke up in.

"Good morning little sister." Someone said. I flinched and turned around to see Sebastian standing in the doorway.

"Where are we?" I asked.

"Somewhere far away. Somewhere where no one will be able to find us." He said.

I exhaled deeply. This was just like last time. Maybe this was going to be worst, but it was for the best at the same time.

"You look confused. Do you want me to explain to you everything that happened last night?" Sebastian asked. I shook my head.

"I do remember. That's the problem." I responded. Sebastian closed his eyes for a second. He opened his eyes again and took a deep breath.

"Do you want some breakfast? I have some made in the kitchen."

"The only hallway this place has is a dead end. Where the hell is the kitchen?" I asked.

"Come on, you'll love this." Sebastian said and started to walk out into the hallway.

"Amuse me," I mumbled as I followed him. He walked towards the end of the hallway. He looked at me over his shoulder and said "Remember this so you don't get lost next time you come up here." I nodded. He turned the knob of the last room down the hallway and entered inside. I followed him. We ended up entering an empty, spare room. Sebastian walked over to the other side of the room to another door. He took out a key from his pocket. He entered the key to the door knob and pushed the door open. I took a closer look at what was inside it. It was a door leading to stairs that were going down. So this was how I will get downstairs.

"You're right. This is pretty amazing." I said. Sebastian smirked. We both made our way down the stairs. As we got to the end of it, I noticed that we were on the first floor. There was a living room, a kitchen, a bathroom, closets and a front door, surprisingly. It was kind of like the one Jace, Sebastian and I were at last time. But this time, it was completely different, Jace, the other half of my soul, wasn't here. I was afraid that I would never see him again. But if it was to keep him alive, so be it. I would try to survive no matter how much I will die inside from now on. We both walked over to the kitchen. Sebastian was right. He had already prepared breakfast. The table was set up already. He had made eggs and bacon.

"I never thought you would make food smell this good." I said as I slid on the chair.

Sebastian grinned as he sat on the chair across from me and said "You don't even know the other side of me little sister."

"Oh, so you have another side? What side is that called? The Unknown side?" I joked. He laughed. I had to try and get along with him. He was indeed, my brother, and I had to stay with him for only Angel Raziel knows how long.

"Yes, the unknown side. Every person has two sides of them. I know you do little sister. You have a nice and girly side. Then there's the side where you could kill every human being on earth if Jace were to be in danger." He said.

I bit my lip, he was right. I would do anything just for Jace. Jace. My Jace. My killer, hot, blond shadowhunter. I wish he was next to me right now. I wish I could count on him. But for now, our bond was broken. I wondered if he was thinking about me this moment the way I was thinking about him.  
"Yeah, I guess I do. I am like you, in a way, if that's even possible." I said. I started to eat. Sebastian just stared at me. He was clearly thinking of something.

"Have you ever thought about what it would be like If I was never born?" He asked.

I nearly choked on the food I was swallowing. "_What?"_ I asked.

"You heard me." He responded. I inhaled deeply.

"Yes, I have. I've thought about it many times that I can't count them all. But I have come to this conclusion, if you weren't born, our parents would have never gotten together, then I wouldn't have been born either." I said. Sebastian nodded.

"Clary, I know what you think of me. I know what everyone thinks of me. It feels pretty cool, being evil and all, but I sometimes get so lonely. Knowing that I will never be able to marry someone and build a family." He said. His words hit me really hard on the gut. I never imagined Sebastian wanting to marry someone or build a family.

"I'm sorry." Was all I said. I didn't know _what_ to say. I kind of felt pity for him.

"It's okay. It's not your fault. It's our fathers." He said and started to eat. He was right. Valentine made Sebastian turn into a monster before he was even born.

"Sebastian… Jonathan?" I asked. I never got used to the idea of calling him by his real name.

"Yeah?"

"Am I ever going to go back?" I asked.

He inhaled deeply and stayed silent for a minute. "It depends. IF I succeed with my plan, I might let you go. If not, then no. You are my sister Clary, we are the last of the Morgenstern's and I won't lose you. I lost our mother from the moment I was born. I lost our father because the angel killed him. I won't lose you." He said.

I took a deep breath to what he just said. Sebastian slid off his chair and walked back upstairs. This time, I didn't follow him. I started to feel numb. My worlds were colliding, once again. I built these walls around me to protect myself from the dark, and now, to watch them crumble down, it changes things. Would it be possible that I am once again tempted by darkness?


End file.
